small bug in docs #785
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python application | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| setup: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest | |
| pip install . | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Cache pip packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| test_lfq: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install package | |
| run: pip install . | |
| - name: Test LFQ dataset | |
| run: | | |
| wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/LFQ_PXD007683.zip | |
| unzip -d ./lfq LFQ_PXD007683.zip | |
| multiqc --quantms-plugin ./lfq --config ./lfq/multiqc_config.yml -o ./results_lfq | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_lfq | |
| path: ./results_lfq | |
| test_tmt: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install package | |
| run: pip install . | |
| - name: Test TMT dataset | |
| run: | | |
| wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/TMT_PXD007683.zip | |
| unzip -d ./tmt TMT_PXD007683.zip | |
| multiqc --quantms-plugin ./tmt --config ./tmt/multiqc_config.yml -o ./results_tmt | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_tmt | |
| path: ./results_tmt | |
| test_dia: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install package | |
| run: pip install . | |
| - name: Test quantms DIA dataset | |
| run: | | |
| wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/dia/dia.zip | |
| unzip -d ./dia dia.zip | |
| multiqc --quantms-plugin ./dia --config ./dia/multiqc_config.yml -o ./results_dia | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_dia | |
| path: ./results_dia | |
| test_diann: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install package | |
| run: pip install . | |
| - name: Test DIANN dataset | |
| run: | | |
| wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/PXD063291.zip | |
| unzip PXD063291.zip | |
| multiqc --diann-plugin ./PXD063291 -o ./results_diann | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_diann | |
| path: ./results_diann | |
| test_mzid_mzML: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install package | |
| run: pip install . | |
| - name: Test mzid & mzML file | |
| run: | | |
| mkdir -p ~/mzid_mzML | |
| wget -nv -P ~/mzid_mzML https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD053068/F10854.mzML | |
| wget -nv -P ~/mzid_mzML https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD053068/F10854.mzid.gz | |
| wget -nv -P ~/mzid_mzML https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD053068/Q00745.mzML | |
| wget -nv -P ~/mzid_mzML https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD053068/Q00745.mzid.gz | |
| wget -nv -P ~/mzid_mzML https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD053068/cGAS.mzML | |
| wget -nv -P ~/mzid_mzML https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD053068/cGAS.mzid.gz | |
| # wget -nv -P ~/mzid_mzML https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD053068/Insulin-1.mzML | |
| # wget -nv -P ~/mzid_mzML https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD053068/insulin-1.mzid.gz | |
| # wget -nv -P ~/mzid_mzML https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD053068/Insulin-2.mzML | |
| # wget -nv -P ~/mzid_mzML https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD053068/insulin-2.mzid.gz | |
| gunzip ~/mzid_mzML/*.mzid.gz | |
| multiqc --mzid-plugin ~/mzid_mzML -o ./results_mzid_mzML | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_mzid_mzML | |
| path: ./results_mzid_mzML | |
| test_mzid_mgf: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python "3.10" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install package | |
| run: pip install . | |
| - name: Test mzid & MGF file | |
| run: | | |
| mkdir -p ~/mzid_mgf | |
| wget -nv -P ~/mzid_mgf https://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD054720/F001234.mgf | |
| wget -nv -P ~/mzid_mgf https://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD054720/F001235.mgf | |
| wget -nv -P ~/mzid_mgf https://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD054720/F001234.mzid.gz | |
| wget -nv -P ~/mzid_mgf https://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD054720/F001235.mzid.gz | |
| gunzip ~/mzid_mgf/*mzid.gz | |
| multiqc --mzid-plugin ~/mzid_mgf -o ./results_mzid_mgf | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_mzid_mgf | |
| path: ./results_mzid_mgf | |
| test_maxquant: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python "3.10" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install package | |
| run: pip install . | |
| - name: Test MaxQuant file | |
| run: | | |
| wget -nv https://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip | |
| unzip -d ./maxquant txt_20min.zip | |
| multiqc --maxquant-plugin ./maxquant -o ./results_maxquant | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_maxquant | |
| path: ./results_maxquant | |
| test_maxquant_dia: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python "3.10" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install package | |
| run: pip install . | |
| - name: Test MaxQuant DIA file | |
| run: | | |
| wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/maxquant/MaxDIA_txt.zip | |
| mkdir -p ./maxdia | |
| unzip -d ./maxdia MaxDIA_txt.zip | |
| multiqc --maxquant-plugin ./maxdia -o ./results_maxquant_dia | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_maxquant_dia | |
| path: ./results_maxquant_dia | |
| test_proteobench: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python "3.10" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install package | |
| run: pip install . | |
| - name: Test ProteoBench file | |
| run: | | |
| wget -nv --no-check-certificate https://proteobench.cubimed.rub.de/datasets/d01e87b997b84c985868204b1ed26749902fd7f9/d01e87b997b84c985868204b1ed26749902fd7f9_data.zip | |
| unzip -d ./proteobench d01e87b997b84c985868204b1ed26749902fd7f9_data.zip | |
| multiqc --proteobench-plugin ./proteobench -o ./results_proteobench | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_proteobench | |
| path: ./results_proteobench | |
| test_fragpipe: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python "3.10" | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install package | |
| run: pip install . | |
| - name: Test FragPipe file | |
| run: | | |
| wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/PXD062399.zip | |
| mkdir -p ./fragpipe | |
| unzip -d ./fragpipe PXD062399.zip | |
| multiqc --fragpipe-plugin ./fragpipe -o ./results_fragpipe | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_fragpipe | |
| path: ./results_fragpipe | |
| test_big_dia: | |
| needs: setup | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install package | |
| run: pip install . | |
| - name: Test big quantms DIA dataset | |
| run: | | |
| wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/PXD062383.zip | |
| unzip -d ./PXD062383 PXD062383.zip | |
| multiqc --quantms-plugin ./PXD062383 --config ./PXD062383/multiqc_config.yml -o ./results_big_dia | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_big_dia | |
| path: ./results_big_dia |